Retrotransposon markers are components of DNA which are used as

cladistic Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived ch ...

markers. They assist in determining the common

ancestry An ancestor, also known as a forefather, fore-elder or a forebear, is a parent or ( recursively) the parent of an antecedent (i.e., a grandparent, great-grandparent, great-great-grandparent and so forth). ''Ancestor'' is "any person from wh ...

, or not, of related

taxa In biology, a taxon ( back-formation from '' taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular n ...

. The "presence" of a given retrotransposon in related taxa suggests their orthologous integration, a derived condition acquired via a common ancestry, while the "absence" of particular elements indicates the

plesiomorphic In phylogenetics, a plesiomorphy ("near form") and symplesiomorphy are synonyms for an ancestral character shared by all members of a clade, which does not distinguish the clade from other clades. Plesiomorphy, symplesiomorphy, apomorphy, an ...

condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology of mammals depends on the availability of retrotransposons that were actively integrating before the divergence of a particular

species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...

Details

The analysis of

SINE In mathematics, sine and cosine are trigonometric functions of an angle. The sine and cosine of an acute angle are defined in the context of a right triangle: for the specified angle, its sine is the ratio of the length of the side that is opp ...

s – Short INterspersed Elements –

LINE Line most often refers to: * Line (geometry), object with zero thickness and curvature that stretches to infinity * Telephone line, a single-user circuit on a telephone communication system Line, lines, The Line, or LINE may also refer to: Art ...

s – Long INterspersed Elements – or truncated LTRs – Long Terminal Repeats – as molecular

markers represents a particularly interesting complement to

DNA sequence DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...

and morphological data. The reason for this is that retrotransposons are assumed to represent powerful noise-poor

synapomorphies In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to hav ...

. The target sites are relatively unspecific so that the chance of an independent integration of exactly the same element into one specific site in different

is not large and may even be negligible over

evolutionary Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation t ...

time scales. Retrotransposon integrations are currently assumed to be irreversible events; this might change since no eminent biological mechanisms have yet been described for the precise re-excision of class I

transposon A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transp ...

s, but see van de Lagemaat ''et al.'' (2005). A clear differentiation between

ancestral An ancestor, also known as a forefather, fore-elder or a forebear, is a parent or ( recursively) the parent of an antecedent (i.e., a grandparent, great-grandparent, great-great-grandparent and so forth). ''Ancestor'' is "any person from w ...

and derived character state at the respective locus thus becomes possible as the absence of the introduced sequence can be with high confidence considered ancestral. In combination, the low incidence of

homoplasy Homoplasy, in biology and phylogenetics, is the term used to describe a feature that has been gained or lost independently in separate lineages over the course of evolution. This is different from homology, which is the term used to characterize ...

together with a clear character polarity make retrotransposon integration markers ideal tools for determining the common

by a shared derived transpositional event. The "presence" of a given retrotransposon in related taxa suggests their orthologous integration, a derived condition acquired via a common ancestry, while the "absence" of particular elements indicates the

. Examples for

phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...

studies based on retrotransposon presence/absence data are the definition of

whales Whales are a widely distributed and diverse group of fully aquatic placental marine mammals. As an informal and colloquial grouping, they correspond to large members of the infraorder Cetacea, i.e. all cetaceans apart from dolphins a ...

as members of the order

Cetartiodactyla The even-toed ungulates (Artiodactyla , ) are ungulates—hoofed animals—which bear weight equally on two (an even number) of their five toes: the third and fourth. The other three toes are either present, absent, vestigial, or pointing poster ...

with hippos being their closest living relatives, hominoid relationships, the

strepsirrhine Strepsirrhini or Strepsirhini (; ) is a Order (biology), suborder of primates that includes the Lemuriformes, lemuriform primates, which consist of the lemurs of Fauna of Madagascar, Madagascar, galagos ("bushbabies") and pottos from Fauna of A ...

tree, the

marsupial Marsupials are any members of the mammalian infraclass Marsupialia. All extant marsupials are endemic to Australasia, Wallacea and the Americas. A distinctive characteristic common to most of these species is that the young are carried in a ...

radiation from South America to Australia, and the placental

mammalian Mammals () are a group of vertebrate animals constituting the class Mammalia (), characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or ...

evolution. Inter-retrotransposons amplified polymorphisms (IRAPs) are alternative retrotransposon-based markers. In this method,

PCR PCR or pcr may refer to: Science * Phosphocreatine, a phosphorylated creatine molecule * Principal component regression, a statistical technique Medicine * Polymerase chain reaction ** COVID-19 testing, often performed using the polymerase chain r ...

oligonucleotide primers face outwards from terminal retrotransposon regions. Thus, they amplify the fragment between two retrotransposon insertions. As retrotransposon integration patterns vary between genotypes, the number and size of the resulting amplicons can be used for differentiation of genotypes or cultivars, to measure genetic diversity or to reconstruct phylogenies. SINEs, which are small in size and often integrate within or next to genes represent an optimal source for the generation of effective IRAP markers.

References

{{DEFAULTSORT:Retrotransposon Marker Phylogenetics